The RNA Wave 2000 MicroRNAs (miRNAs) have been identified as a major class of human small RNAs, single-stranded RNAs, 21–25 nucleotides (nts) in length. The 3′ untranslated regions (UTRs) of messenger RNAs (mRNAs) are targeted by miRNAs through imperfect base pairing (Fujii 2017). Although we discovered miRNAs (Omoto and Fujii 2006; Fujii 2017), it is now well known that resident miRNAs repress gene expression at the translational and transcriptional levels. miRNAs as noncoding genes (genomic miRNAs) are transcribed from intergenic and intronic regions, and also the protein- coding sites (CDS) of the human genome (as DNA) and RNA virus genome. miR- NAs in exosome are mobile genetic elements because they are secreted from cells We only see what we know. —von Goethe JW © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 Y. R. Fujii, The MicroRNA Quantum Code Book, https://doi.org/10.1007/978-981-19-8586-7_1 2 Fig. 1.1 Preparation of idea for miRNA function analysis into circulation, horizontally transmitted to other cells, and vertically transmitted from mother to fetus. Below is a validated RNA wave 2000 model (Fujii 2008, 2017). (1) miRNA genes are mobile genetic elements that induce transcriptional and posttranscriptional silencing through network processes. (2) RNA information provided by miRNA genes is affected by the global environment and the life cycles and spreads intracellularly, intercellularly, intraorganically, interorganically, in intraspecies, and in interspecies. (3) Mobile miRNAs are self-propagating and (4) cells contain resident and genomic miRNAs. Therefore, we hypothesized that most of all biological processes, including human diseases, are programmed and con- trolled by the miRNA code (Fig. 1.1). Elements required for elucidation of the quantum miRNA code are indicated in Fig. 1.1 (numbers 1–7). Among them, the elements related to computer science account for Nos. 3–7, and the key is Nos. 1 and 2, miRNA biology, and genetics. That is where data bioscience is different from simple data science.
چکیده فارسی
2000 MicroRNA های موج RNA (miRNAs) به عنوان یک کلاس اصلی از RNA های کوچک انسانی، RNA های تک رشته ای، با طول 21-25 نوکلئوتید (NTS) شناسایی شده اند. مناطق ترجمه نشده 3' (UTRs) RNA های پیام رسان (mRNAs) توسط miRNA ها از طریق جفت شدن باز ناقص هدف قرار می گیرند (Fujii 2017). اگرچه ما miRNA ها را کشف کردیم (Omoto و Fujii 2006؛ Fujii 2017)، اکنون به خوبی شناخته شده است که miRNA های ساکن بیان ژن را در سطوح ترجمه و رونویسی سرکوب می کنند. miRNA ها به عنوان ژن های غیر کد کننده (miRNA های ژنومی) از مناطق بین ژنی و اینترونیک و همچنین مکان های کد کننده پروتئین (CDS) ژنوم انسان (به عنوان DNA) و ژنوم ویروس RNA رونویسی می شوند. miR- NAها در اگزوزوم عناصر ژنتیکی متحرک هستند زیرا از سلول‌ها ترشح می‌شوند و ما فقط آنچه را می‌دانیم می‌بینیم. —فون گوته JW © نویسنده(ها)، تحت مجوز انحصاری Springer Nature Singapore Pte Ltd. 2023 Y. R. Fujii, The MicroRNA Quantum Code Book, https://doi.org/10.1007/978-981-19-8586-7_1 2 شکل 1.1 آماده سازی ایده برای تجزیه و تحلیل عملکرد miRNA در گردش خون، به صورت افقی به سلول های دیگر و به صورت عمودی از مادر به جنین منتقل می شود. در زیر مدل 2000 موج RNA معتبر (Fujii 2008، 2017) وجود دارد. (1) ژن‌های miRNA عناصر ژنتیکی متحرکی هستند که خاموشی رونویسی و پس از رونویسی را از طریق فرآیندهای شبکه القا می‌کنند. (2) اطلاعات RNA ارائه شده توسط ژن های miRNA تحت تأثیر محیط جهانی و چرخه های زندگی قرار می گیرد و به صورت درون سلولی، بین سلولی، درون ارگانی، بین ارگانی، درون گونه ای و بین گونه ای پخش می شود. (3) miRNA های متحرک خود تکثیر می شوند و (4) سلول ها حاوی miRNA های ساکن و ژنومی هستند. بنابراین، ما فرض کردیم که بیشتر فرآیندهای بیولوژیکی، از جمله بیماری‌های انسانی، توسط کد miRNA برنامه‌ریزی و کنترل می‌شوند (شکل 1.1). عناصر مورد نیاز برای روشن شدن کد miRNA کوانتومی در شکل 1.1 نشان داده شده است (اعداد 1-7). در میان آنها، عناصر مربوط به علوم کامپیوتر شماره های 3-7 را به خود اختصاص می دهند و کلید شماره های 1 و 2، زیست شناسی miRNA و ژنتیک است. اینجاست که علوم زیستی داده با علم داده ساده متفاوت است.
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RNA Gene Information In doing so, algorithms are needed to decode the miRNA code and elucidate the pathogenesis of human diseases (Fujii 2008). miRNAs target multi-mRNAs, and targets are regulated by multi-miRNAs. In language, a word also has multiple mean- ings, and a meaning is shown by multiple words. A “miRNA” is like a “language” (Fig. 1.2). It is a far cry from protein coding, which is a one-to-one algorithm as von Neumann-type linear map. 1 RNA Controls RNA 3 Fig. 1.2 Language and microRNA Therefore, this system corresponds to a nonlinear mapping model of determinis- tic chaos. “Language” is defined in the Cambridge Business English Dictionary as “A particular style of speaking or writing, for example, one that is used by the peo- ple doing a particular job.” Cambridge Advanced Learner’s Dictionary and Thesaurus state “The special words and phrases used by people who do a particular type of work” and “In computer programming, a language is a system of writing instructions for computers” (Cambridge Academic Content Dictionary). There is no mention of “information,” but language is information. Like dictionaries, computer science requires information analysis and is based on computer programming, quantum computing, artificial intelligence (AI), statistics, and linear algebra (Fig. 1.1). If miRNAs are inherited genes, they are both informational, so much scientific evidence is needed to prove the single proposition that “microRNA lan- guages are genes” (Fig. 1.3). However, the word “gene” in the dictionary refers to “A part of the DNA in a cell that controls the physical development behavior, etc. of an individual plant or ani- mal and is passed on from its parents” and “A specific chemical pattern on a chro- mosome that is received from the parents and controls the development of particular characteristics in animal or plant.” There is no description of information, but it is well known that genes are information. Since miRNAs have biological functions such as tumorigenesis and tumor suppression, we hypothesized that chromosomal RNA genes exist similar to retrovirus genomes (Fujii 2009). Retrovirus information was part of DNA and part of RNA, so microRNA information, like language, should be encoded from DNA (genomic) and RNA (resident). 1.2 RNA Gene Information 4 Fig. 1.3 Solo proposition 1.3 Torus Furthermore, we introduced the novel idea that RNA information is contained in a multidimensional “torus” (Fig. 1.4) (Fujii 2010). We reported that circular RNAs (circRNAs) are present in our biological sys- tems, such as the retrovirus proviral genome (Fujii 2010). When miRNAs form a torus, electrons on circular miRNAs move from one base to another adjacent base. Electron can spin around. The direction of the magnetic field rises and falls depend- ing on the direction of the rotating electrons. The superposition of magnetic orienta- tion in each layered miRNA can encode multidimensional RNA information according to quantum theories as quantum computing. We noted that the informa- tion contained in RNA is physics (Fujii 2010), so we created miRNA codes using quantum computing algorithms. The miRNA language in our life is part of quan- tum code. 1 RNA Controls RNA 5 Fig. 1.4 Torus is a novel ide
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